Murray Patterson

Postdoctoral Researcher

Experimental Algorithmics Lab (AlgoLab)
Dipartimento di Informatica Sistemistica e Comunicazione (DISCo)
Università degli Studi di Milano-Bicocca
Edificio U14, Viale Sarca, 336
20126 Milano (Italy)

office: 1001
tel: (+39) 026 448 7917
email: murray[dot]patterson[at]unimib[dot]it


Since summer 2016, I am a postdoctoral fellow in the Experimental Algorithmics Lab at the University of Milano-Bicocca with Gianluca Della Vedova and Paola Bonizzoni. My project is on haplotyping and cancer phylogenies.

From the spring of 2014 I did a 2-year postdoctoral fellowship at the LBBE as part of the Ancestrome Project with Daniel Kahn and Vincent Daubin. My project was on the evolution of metabolic networks from the perspective of the enzymes that catalyse reactions, but also of the structure of the network itself.

From the beginning of 2012 I was an ERCIM fellow with a 2-year Marie Curie ABCDE fellowship. I held my first year of the fellowship with the INRIA at the Laboratoire de Biométrie et Biologie Évolutive (LBBE) of the Université de Lyon in France with Eric Tannier. I held my second year in the Life Sciences Group at the CWI with Alexander Shoenhuth and Gunnar Klau.


Publications



View also at Google Scholar, DBLP or see my full CV, among a list of supporting documents


Current Preprints

Simone Ciccolella, Mauricio Soto Gomez, Murray Patterson, Gianluca Della Vedova, Iman Hajirasouliha and Paola Bonizzoni. Inferring Cancer Progression from Single Cell Sequencing while allowing loss of mutations. bioRxiv, 268243 (2018). doi: 10.1101/268243

Marcel Martin*, Murray Patterson*, Shilpa Garg, Sarah O. Fischer, Nadia Pisanti, Gunnar W. Klau, Alexander Schönhuth and Tobias Marschall. WhatsHap: fast and accurate read-based phasing. bioRxiv, 085050 (2016). doi: 10.1101/085050

Murray Patterson, Thomas Bernard and Daniel Kahn. Correlated Evolution of Metabolic Functions over the Tree of Life. bioRxiv, 093591 (2016). doi: 10.1101/093591

Journal Articles

Stefano Beretta*, Murray Patterson*, Simone Zaccaria, Gianluca Della Vedova and Paola Bonizzoni. HapCHAT: Adaptive haplotype assembly for efficiently leveraging high coverage in long reads. BMC Bioinformatics, 19(1):252 (2018). doi: 10.1186/s12859-018-2253-8

Wandrille Duchemin, Yoann Anselmetti, Murray Patterson, Yann Ponty, Sèverine Bérard, Cedric Chauve, Celine Scornavacca, Vincent Daubin, Eric Tannier. DeCoSTAR: Reconstructing the ancestral organization of genes or genomes using reconciled phylogenies. Genome Biology and Evolution, 9(5):1312—1319 (2017). doi: 10.1093/gbe/evx069

Andrea Bracciali, Marco Aldinucci, Murray Patterson, Tobias Marschall, Nadia Pisanti, Ivan Merelli and Massimo Torquati. pWhatsHap: efficient haplotyping for future generation sequencing. BMC Bioinformatics, 17(11):342 (2016). doi: 10.1186/s12859-016-1170-y

Murray Patterson*, Tobias Marschall*, Nadia Pisanti, Leo van Iersel, Leen Stougie, Gunnar W. Klau+ and Alexander Schonhuth+. WhatsHap: Weighted haplotype assembly for future-generation sequencing reads. Journal of Computational Biology, 22(6):498—509 (2015). doi: 10.1089/cmb.2014.0157

Murray Patterson, Gergely Szöllősi, Vincent Daubin and Eric Tannier. Lateral Gene Transfer, Rearrangement, Reconciliation. BMC Bioinformatics, 14(15):S4 (2013). doi: 10.1186/1471-2105-14-S15-S4

Mohammed El-Kebir*, Tobias Marschall*, Inken Wohlers*, Murray Patterson, Jaap Heringa, Alexander Schönhuth and Gunnar W. Klau. Mapping proteins in the presence of paralogs using units of coevolution. BMC Bioinformatics, 14(15):S18 (2013). doi: 10.1186/1471-2105-14-S15-S18

Ján Maňuch*, Murray Patterson*, Roland Wittler*, Cedric Chauve and Eric Tannier. Linearization of ancestral multichromosomal genomes. BMC Bioinformatics, 13(19):S11 (2012). doi: 10.1186/1471-2105-13-S19-S11

Ján Maňuch*, Murray Patterson* and Cedric Chauve. Hardness results on the gapped consecutive-ones property problem. Discrete Applied Mathematics, 160(18):2760—2768 (2012). doi: 10.1016/j.dam.2012.03.019

Ján Maňuch* and Murray Patterson*. The complexity of the gapped consecutive-ones property problem for matrices of bounded maximum degree. Journal of Computational Biology, 18(9):1243—1253 (2011). doi: 10.1089/cmb.2011.0128

Roland Wittler, Ján Maňuch*, Murray Patterson* and Jens Stoye. Consistency of sequence-based gene clusters. Journal of Computational Biology, 18(9):1023—1039 (2011). doi: 10.1089/cmb.2011.0083

Refereed Conference Proceedings

Simone Ciccolella, Mauricio Soto, Murray Patterson, Gianluca Della Vedova, Iman Hajirasouliha and Paola Bonizzoni. gpps: An ILP-based approach for inferring cancer progression with mutation losses from single cell data. In proceedings of the 8th IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS, Las Vegas, USA, 2018), to appear.

Gianluca Della Vedova*, Murray Patterson*, Raffaella Rizzi* and Mauricio Soto*. Character-based Phylogeny Construction and its Application to Tumor Evolution. In Proceedings of the 13th Conference on Computability in Europe (CiE, Turku, Finland, 2017), LNCS 10307:3-13 (2017). doi: 10.1007/978-3-319-58741-7_1

Marco Aldinucci, Andrea Bracciali, Tobias Marschall, Murray Patterson, Nadia Pisanti and Massimo Torquati. High-Performance Haplotype Assembly. In Post Conference Proceedings of the 11th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB, Cambridge, UK, 2014), LNCS 8623:245—258 (2015). doi: 10.1007/978-3-319-24462-4_21

Murray Patterson*, Tobias Marschall*, Nadia Pisanti, Leo van Iersel, Leen Stougie, Gunnar W. Klau+ and Alexander Schönhuth+. WhatsHap: Haplotype assembly for future-generation sequencing reads. In Proceedings of the 18th Annual International Conference on Research in Computational Molecular Biology (RECOMB, Pittsburgh PA, USA, 2014), LNCS 8394:237—249 (2014). doi: 10.1007/978-3-319-05269-4_19

Cedric Chauve*, Murray Patterson* and Ashok Rajaraman*. Hypergraph covering problems motivated by genome assembly questions. In Proceedings of the International Workshop on Combinatorial Algorithms (IWOCA, Rouen, France, 2013), LNCS 8288:428—432 (2013). doi: 10.1007/978-3-642-45278-9_37

Ján Maňuch*, Murray Patterson*, Roland Wittler*, Cedric Chauve and Eric Tannier. Linearization of ancestral multichromosomal genomes. In Proceedings of the 12th Annual Cologne-Twente Workshop on Graphs and Combinatorial Optimization (CTW, Enschede, The Netherlands, 2013), 169—173 (2013).

Cedric Chauve*, Ján Maňuch*, Murray Patterson* and Roland Wittler*. Tractability results for the consecutive-ones property with multiplicity. In Proceedings of the 22nd Annual Symposium on Combinatorial Pattern Matching (CPM, Palermo, Italy, 2011), LNCS 6661:90—103 (2011). doi: 10.1007/978-3-642-21458-5_10

Ján Maňuch*, Murray Patterson* and Arvind Gupta. Towards a characterization of the generalized cladistic character compatibility problem for non-branching character trees. In Proceedings of the 7th International Symposium on Bioinformatics Research and Applications (ISBRA, Changsha, China, 2011), LNCS 6674:440—451 (2011).

Ján Maňuch* and Murray Patterson*. The complexity of the gapped consecutive-ones property problem for matrices of bounded maximum degree. In Proceedings of the 8th Annual RECOMB Comparative Genomics (Ottawa, Canada, 2010), LNBI 6398:278—289 (2010).

Ján Maňuch*, Murray Patterson*, Sheung-Hung Poon* and Chris Thachuk*. Complexity of finding non-planar rectilinear drawings of graphs. In Proceedings of the 18th International Symposium on Graph Drawing (GD, Konstanz, Germany, 2010), LNCS 6502:305—316 (2011). doi: 10.1007/978-3-642-18469-7_28

Cedric Chauve*, Ján Maňuch* and Murray Patterson*. On the gapped consecutive-ones property. In Proceedings of the European Conference on Combinatorics, Graph Theory and Applications (EuroComb, Bordeaux, France, 2009), ENDM 34:121—125 (2009). doi: 10.1016/j.endm.2009.07.020

Ján Maňuch*, Murray Patterson* and Arvind Gupta. On the generalised character compatibility problem for non-branching character trees. In Proceedings of the 15th Annual International Computing and Combinatorics Conference (COCOON, Niagara Falls, USA, 2009), LNCS 5609:268—276 (2009). doi: 10.1007/978-3-642-02882-3_27

Murray Patterson, Yongmei Liu, Eugenia Ternovska and Arvind Gupta. Grounding for model expansion in k-guarded formulas with inductive definitions. In Proceedings of the 20th International Joint Conferences on Artificial Intelligence (IJCAI, Hyderabad, India, 2007), 161—166 (2007).

Theses

Murray Patterson. Variants of the consecutive-ones property motivated by the reconstruction of ancestral species. PhD Thesis, Department of Computer Science, University of British Columbia, Canada, 2012. doi: 10.14288/1.0052159

Murray Patterson. Grounding for model expansion in k-guarded formulas. Masters Thesis, Department of Computing Science, Simon Fraser University, Canada, 2006.

Murray Patterson. Implementing Runge-Kutta solvers in Java. Bachelor of Science Honours Thesis, Department of Computer Science, Acadia University, Canada, 2003.

In any publication listing containing a *, this indicates that all authors whose names are followed by a * have contributed equally to this publication. In order to be consistent, this means that for papers that list the names of authors alphabetically (which is a common practice amongst computer science and theoretical bioinformatics papers), there is a * following every name.


Education



2006—2011 Doctor of Philosophy, Department of Computer Science, University of British Columbia, Vancouver, Canada, GPA — 4.0/4.
Advisors: Ján Maňuch, Cedric Chauve and Arvind Gupta
2004—2006 Master of Science, School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada, GPA — 3.9/4.
Advisors: Eugenia Ternovska and Arvind Gupta
1999—2003 Bachelor of Computer Science (Honours), Jodrey School of Computer Science, Acadia University, Wolfville, Nova Scotia, Canada, GPA — 3.8/4 (top 5%).
Advisors: Raymond J. Spiteri and Jim Diamond

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